Package | Description |
---|---|
com.compomics.util.experiment.biology.genes |
Classes related to genes.
|
com.compomics.util.experiment.biology.proteins |
Classes related to proteins.
|
com.compomics.util.experiment.identification |
Experiment classes related to identifications.
|
com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
com.compomics.util.experiment.identification.utils |
Modifier and Type | Method and Description |
---|---|
GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
|
Modifier and Type | Method and Description |
---|---|
HashSet<Integer> |
Peptide.getPotentialModificationSites(Modification modification,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as a set.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.buildPeptidesAndProteins(SpectrumMatch spectrumMatch,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceProvider sequenceProvider)
Creates the peptides and protein instances based on the given spectrum
match.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceProvider sequenceProvider)
Validates a peptide depending on its protein inference status.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Class and Description |
---|---|
class |
FMIndex
The FM index.
|
Modifier and Type | Method and Description |
---|---|
static TreeMap<String,String[]> |
PeptideUtils.getAaAfter(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaAfter(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string.
|
static TreeMap<String,String[]> |
PeptideUtils.getAaBefore(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaBefore(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static boolean |
PeptideUtils.isDecoy(Peptide peptide,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the peptide matches a decoy
sequence.
|
static boolean |
ProteinUtils.isDecoy(String accession,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.
|
static boolean |
PeptideUtils.isEnzymatic(Peptide peptide,
SequenceProvider sequenceProvider,
ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.
|
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